LRRprofiler_v0.2_sing_3.6.def

BootStrap: library
From: ubuntu:18.04


%help

This container launches the LRRprofiler pipeline used to annot proteins with Leucine Rich Repeat motifs.
=======================================================================================

    usage (help)   : singularity run LRRprofiler_v0.1.sif
    usage (basic)  : singularity run LRRprofiler_v0.1.sif --in_proteome <fasta file> --name <string>
    usage (example): singularity run LRRprofiler_v0.1.sif --in_proteome example/Arabidopsis_Thaliana_reviewed_proteom_SwissProt_05-2020.fasta --name ARATH 

    building container : singularity build LRRprofiler_v0.1.sif LRRprofiler_v0.1_sing_3.6.def

For more details please see the pipeline documentation pages on the LRRprofiler website:
==================================================================================
#https://github.com/cgottin/LRRprofiler


If you use this pipeline please cite:
=====================================

	--------------------------------------
MAFFT v7.271 
	Katoh K., Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780. Edgar R.C. (2004). 

SMART database
	Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922

HMMER v3.1b2
	S. R. Eddy. (2011) Accelerated profile HMM searches. PLoS Comp. Biol., 7:e1002195

iTAK 
	Zheng Yet al. (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant 9:1667-1670.
	--------------------------------------

%files
	tmhmm2.0c.tar

%post
	apt-get -y update
	apt-get -y install software-properties-common
	add-apt-repository universe
	apt-get -y update 
	apt-get -y install python3-biopython
	apt-get -y install gawk
	apt-get -y install unzip
	apt-get -y install wget
	apt-get -y install hmmer
	apt-get -y install mafft
	apt-get -y install pandoc-data
	apt-get -y install pandoc
	apt-get -y install bioperl
	#apt-get -y install subversion
	apt-get -y install git
	apt-get -y update

## getting scripts from github
	#svn checkout https://github.com/kentnf/iTAK/trunk/
	#mv trunk iTAK
	git clone https://github.com/kentnf/iTAK.git
	chmod -R 777 /iTAK/

	git clone --single-branch --branch master https://github.com/cgottin/LRRprofiler.git
	chmod 777 /LRRprofiler/src/*

	tar -xf /tmhmm2.0c.tar
	chmod -R 777 /tmhmm2.0c/

	apt-get purge -y --auto-remove wget unzip git #subversion

# running iTAK on test set to set up files
	perl /iTAK/iTAK.pl /iTAK/test_seq

	apt-get -y install r-base
	apt-get -y install r-base-dev
	R --slave -e 'install.packages(c("rmarkdown","ggplot2","reshape2"))'

	rm -rf /var/lib/apt/lists/*
	apt-get clean


%environment
	export LC_ALL=C
	export LG_SCRIPT="/LRRprofiler/src"
	export LG_HMMlib="/LRRprofiler/HMM_lib"
	export LG_MAFFT="mafft"
	export LG_ITAK="/iTAK/iTAK.pl"
	export LG_TMHMM="/tmhmm2.0c/bin/tmhmm"
	R_VERSION=3.6.1
	export R_VERSION
	R_CONFIG_DIR=/etc/R/
	export R_CONFIG_DIR
	export PATH=$PATH


%runscript
	exec bash /LRRprofiler/src/LRRprofiler_global.sh "$@"

%labels
	Author Céline Gottin & Vincent Ranwez